Starting phenix.real_space_refine on Thu Feb 15 03:30:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c2s_16398/02_2024/8c2s_16398_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.423 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 30 5.49 5 S 483 5.16 5 C 41185 2.51 5 N 10513 2.21 5 O 11427 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "G ASP 180": "OD1" <-> "OD2" Residue "G ASP 298": "OD1" <-> "OD2" Residue "G PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 352": "OD1" <-> "OD2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 269": "OE1" <-> "OE2" Residue "O ASP 150": "OD1" <-> "OD2" Residue "P PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 57": "OE1" <-> "OE2" Residue "T GLU 61": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "W GLU 67": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 55": "OE1" <-> "OE2" Residue "a GLU 35": "OE1" <-> "OE2" Residue "a TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 78": "OD1" <-> "OD2" Residue "c GLU 6": "OE1" <-> "OE2" Residue "c GLU 37": "OE1" <-> "OE2" Residue "d ASP 16": "OD1" <-> "OD2" Residue "d ASP 45": "OD1" <-> "OD2" Residue "d PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 29": "OD1" <-> "OD2" Residue "i ASP 107": "OD1" <-> "OD2" Residue "k GLU 20": "OE1" <-> "OE2" Residue "k TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 27": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "p GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 63667 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 933 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "C" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1721 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 15, 'TRANS': 191} Chain: "D" Number of atoms: 3463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3463 Classifications: {'peptide': 430} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 403} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1639 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 188} Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3300 Classifications: {'peptide': 428} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 406} Chain: "G" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5248 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 31, 'TRANS': 656} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2540 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1431 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "J" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1300 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 3, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 737 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4800 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3632 Classifications: {'peptide': 459} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2696 Classifications: {'peptide': 344} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 323} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2607 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 16, 'TRANS': 303} Chain: "P" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2626 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain: "R" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 413 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "S" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 594 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 611 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "U" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'TRANS': 80} Chain: "V" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "W" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 935 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "X" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1396 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 11, 'TRANS': 159} Chain: "Y" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1037 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "Z" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1167 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "a" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 556 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "b" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 628 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 398 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "d" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 996 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 12, 'TRANS': 107} Chain: "e" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "f" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 456 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 850 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "h" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1162 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain: "i" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 787 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 12, 'TRANS': 81} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 537 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 6, 'TRANS': 55} Chain: "k" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "l" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1294 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 18, 'TRANS': 135} Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1050 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 11, 'TRANS': 114} Chain: "n" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1534 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "o" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 979 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 105} Chain: "p" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1424 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain: "r" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 487 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 10, 'TRANS': 50} Chain breaks: 1 Chain: "s" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 269 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "L" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 193 Unusual residues: {'3PE': 1, 'CDL': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "M" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'CDL:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 35 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "U" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'EHZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "d" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "g" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 70 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1688 SG CYS B 129 67.049 106.975 94.080 1.00 45.75 S ATOM 1191 SG CYS B 65 66.237 100.682 92.124 1.00 49.15 S ATOM 1185 SG CYS B 64 61.283 104.105 94.269 1.00 49.27 S ATOM 1918 SG CYS B 159 64.288 105.985 88.797 1.00 48.30 S ATOM 8166 SG CYS E 103 41.138 142.326 31.577 1.00 83.29 S ATOM 8200 SG CYS E 108 37.870 141.832 29.531 1.00 84.77 S ATOM 8484 SG CYS E 144 38.836 145.872 34.750 1.00 83.23 S ATOM 8507 SG CYS E 148 36.150 145.861 33.347 1.00 88.56 S ATOM 11708 SG CYS F 362 46.642 145.575 56.495 1.00 58.26 S ATOM 11728 SG CYS F 365 45.898 142.460 51.846 1.00 58.33 S ATOM 12050 SG CYS F 405 43.093 148.403 51.583 1.00 64.78 S ATOM 11689 SG CYS F 359 49.382 147.391 50.885 1.00 61.60 S ATOM 13128 SG CYS G 114 58.851 133.647 68.052 1.00 34.23 S ATOM 13067 SG CYS G 105 58.661 127.503 66.254 1.00 34.55 S ATOM 13088 SG CYS G 108 63.855 131.100 65.077 1.00 36.44 S ATOM 13460 SG CYS G 156 58.611 143.638 61.995 1.00 41.56 S ATOM 13437 SG CYS G 153 60.015 139.381 57.107 1.00 38.09 S ATOM 13484 SG CYS G 159 63.494 144.632 58.302 1.00 46.81 S ATOM 13813 SG CYS G 203 63.540 139.877 62.581 1.00 42.98 S ATOM 12574 SG CYS G 41 52.775 147.997 64.155 1.00 40.22 S ATOM 12660 SG CYS G 52 51.029 144.402 65.032 1.00 37.88 S ATOM 12685 SG CYS G 55 47.347 147.677 67.472 1.00 41.95 S ATOM 12786 SG CYS G 69 49.606 150.152 65.803 1.00 42.29 S ATOM 21112 SG CYS I 128 64.818 114.245 69.035 1.00 41.87 S ATOM 20759 SG CYS I 82 66.426 118.952 70.909 1.00 44.21 S ATOM 20782 SG CYS I 85 67.926 117.213 73.932 1.00 40.59 S ATOM 20740 SG CYS I 79 71.345 116.024 69.122 1.00 43.07 S ATOM 20759 SG CYS I 82 66.426 118.952 70.909 1.00 44.21 S ATOM 21062 SG CYS I 121 61.839 111.437 81.831 1.00 38.69 S ATOM 21036 SG CYS I 118 67.588 108.336 82.204 1.00 39.74 S ATOM 21083 SG CYS I 124 65.249 111.159 76.749 1.00 39.01 S ATOM 20810 SG CYS I 89 67.155 114.604 81.988 1.00 39.04 S ATOM 40075 SG CYS R 59 63.818 118.032 53.067 1.00 27.40 S ATOM 40251 SG CYS R 84 65.235 119.669 55.331 1.00 31.93 S ATOM 40273 SG CYS R 87 66.641 116.481 54.984 1.00 33.26 S Time building chain proxies: 25.39, per 1000 atoms: 0.40 Number of scatterers: 63667 At special positions: 0 Unit cell: (146.016, 197.392, 298.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 483 16.00 P 30 15.00 O 11427 8.00 N 10513 7.00 C 41185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS X 77 " - pdb=" SG CYS X 109 " distance=2.03 Simple disulfide: pdb=" SG CYS X 87 " - pdb=" SG CYS X 99 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 96 " - pdb=" SG CYS Y 116 " distance=2.03 Simple disulfide: pdb=" SG CYS e 32 " - pdb=" SG CYS e 65 " distance=2.03 Simple disulfide: pdb=" SG CYS e 42 " - pdb=" SG CYS e 55 " distance=2.04 Simple disulfide: pdb=" SG CYS o 58 " - pdb=" SG CYS o 89 " distance=2.03 Simple disulfide: pdb=" SG CYS p 76 " - pdb=" SG CYS p 83 " distance=2.03 Simple disulfide: pdb=" SG CYS p 112 " - pdb=" SG CYS p 124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.40 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 148 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 108 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 103 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 144 " pdb=" FES G 803 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 69 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 52 " pdb="FE2 FES G 803 " - pdb=" SG CYS G 55 " pdb="FE1 FES G 803 " - pdb=" SG CYS G 41 " pdb=" SF4 B 201 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 129 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 159 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 64 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 65 " pdb=" SF4 F 501 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 365 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 359 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 405 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 362 " pdb=" SF4 G 801 " pdb="FE3 SF4 G 801 " - pdb=" NE2 HIS G 101 " pdb="FE1 SF4 G 801 " - pdb=" SG CYS G 114 " pdb="FE4 SF4 G 801 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G 801 " - pdb=" SG CYS G 105 " pdb=" SF4 G 802 " pdb="FE2 SF4 G 802 " - pdb=" SG CYS G 153 " pdb="FE4 SF4 G 802 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G 802 " - pdb=" SG CYS G 156 " pdb="FE3 SF4 G 802 " - pdb=" SG CYS G 159 " pdb=" SF4 I 202 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 82 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 128 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 85 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 79 " pdb=" SF4 I 203 " pdb="FE3 SF4 I 203 " - pdb=" SG CYS I 124 " pdb="FE1 SF4 I 203 " - pdb=" SG CYS I 121 " pdb="FE2 SF4 I 203 " - pdb=" SG CYS I 118 " pdb="FE4 SF4 I 203 " - pdb=" SG CYS I 89 " pdb="FE2 SF4 I 203 " - pdb=" NE2 HIS I 67 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" NE2 HIS R 68 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 84 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 59 " Number of angles added : 3 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14694 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 328 helices and 28 sheets defined 54.5% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.40 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 31 through 34 No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.636A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Proline residue: A 74 - end of helix removed outlier: 5.620A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'B' and resid 36 through 54 removed outlier: 3.758A pdb=" N SER B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.822A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 163 through 178 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'C' and resid 17 through 32 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.652A pdb=" N ILE C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 125 through 137 removed outlier: 4.130A pdb=" N TRP C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU C 131 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.831A pdb=" N GLN D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 87 through 93 removed outlier: 3.721A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.621A pdb=" N ASP D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 132 through 161 Processing helix chain 'D' and resid 165 through 185 removed outlier: 3.804A pdb=" N GLU D 172 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU D 173 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 229 removed outlier: 3.842A pdb=" N ASN D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 257 through 263 removed outlier: 5.045A pdb=" N GLY D 262 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 272 No H-bonds generated for 'chain 'D' and resid 269 through 272' Processing helix chain 'D' and resid 293 through 316 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 342 through 353 Processing helix chain 'D' and resid 394 through 406 removed outlier: 4.224A pdb=" N HIS D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP D 403 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 421 removed outlier: 3.678A pdb=" N GLY D 419 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'E' and resid 25 through 37 removed outlier: 3.855A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.596A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) Proline residue: E 49 - end of helix Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 114 through 124 Processing helix chain 'E' and resid 166 through 177 removed outlier: 3.630A pdb=" N GLU E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 25 No H-bonds generated for 'chain 'F' and resid 23 through 25' Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 53 through 63 Processing helix chain 'F' and resid 75 through 83 removed outlier: 3.660A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET F 82 " --> pdb=" O LYS F 78 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN F 83 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 115 through 128 Processing helix chain 'F' and resid 144 through 159 Processing helix chain 'F' and resid 184 through 187 Processing helix chain 'F' and resid 189 through 197 Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 225 through 229 Processing helix chain 'F' and resid 231 through 237 Processing helix chain 'F' and resid 239 through 243 removed outlier: 4.010A pdb=" N ALA F 243 " --> pdb=" O GLY F 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 243' Processing helix chain 'F' and resid 276 through 282 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 309 through 312 No H-bonds generated for 'chain 'F' and resid 309 through 312' Processing helix chain 'F' and resid 319 through 324 Processing helix chain 'F' and resid 343 through 357 Processing helix chain 'F' and resid 363 through 381 removed outlier: 4.527A pdb=" N ASP F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 400 removed outlier: 3.522A pdb=" N ASP F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 435 Proline residue: F 414 - end of helix removed outlier: 3.947A pdb=" N ARG F 423 " --> pdb=" O ILE F 419 " (cutoff:3.500A) Proline residue: F 424 - end of helix Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.805A pdb=" N LYS G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 265 through 269 Processing helix chain 'G' and resid 271 through 275 Processing helix chain 'G' and resid 296 through 309 removed outlier: 3.786A pdb=" N ARG G 302 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET G 306 " --> pdb=" O ARG G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 314 No H-bonds generated for 'chain 'G' and resid 312 through 314' Processing helix chain 'G' and resid 325 through 338 removed outlier: 3.822A pdb=" N ALA G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 337 " --> pdb=" O ASP G 333 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 357 No H-bonds generated for 'chain 'G' and resid 355 through 357' Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 369 through 371 No H-bonds generated for 'chain 'G' and resid 369 through 371' Processing helix chain 'G' and resid 389 through 401 Processing helix chain 'G' and resid 426 through 434 Processing helix chain 'G' and resid 438 through 445 Processing helix chain 'G' and resid 455 through 459 Processing helix chain 'G' and resid 461 through 480 removed outlier: 4.399A pdb=" N ALA G 464 " --> pdb=" O ASP G 461 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 467 " --> pdb=" O ALA G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 505 removed outlier: 3.668A pdb=" N VAL G 500 " --> pdb=" O ALA G 497 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 516 Processing helix chain 'G' and resid 554 through 556 No H-bonds generated for 'chain 'G' and resid 554 through 556' Processing helix chain 'G' and resid 596 through 606 removed outlier: 3.557A pdb=" N ARG G 601 " --> pdb=" O TRP G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 626 Processing helix chain 'G' and resid 629 through 631 No H-bonds generated for 'chain 'G' and resid 629 through 631' Processing helix chain 'G' and resid 642 through 651 Processing helix chain 'G' and resid 668 through 672 Processing helix chain 'G' and resid 676 through 680 Processing helix chain 'G' and resid 682 through 692 Processing helix chain 'H' and resid 3 through 31 Proline residue: H 12 - end of helix removed outlier: 3.743A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 57 Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 3.972A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 123 removed outlier: 3.669A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 3.558A pdb=" N ALA H 137 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE H 148 " --> pdb=" O VAL H 144 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 170 removed outlier: 3.863A pdb=" N THR H 167 " --> pdb=" O GLN H 163 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 177 No H-bonds generated for 'chain 'H' and resid 174 through 177' Processing helix chain 'H' and resid 179 through 192 removed outlier: 3.637A pdb=" N MET H 184 " --> pdb=" O PRO H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 241 removed outlier: 3.935A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.536A pdb=" N LEU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 310 removed outlier: 4.051A pdb=" N LEU H 294 " --> pdb=" O TRP H 290 " (cutoff:3.500A) Proline residue: H 295 - end of helix removed outlier: 3.545A pdb=" N ALA H 299 " --> pdb=" O PRO H 295 " (cutoff:3.500A) Proline residue: H 308 - end of helix Processing helix chain 'I' and resid 16 through 28 Processing helix chain 'I' and resid 30 through 43 Processing helix chain 'I' and resid 52 through 54 No H-bonds generated for 'chain 'I' and resid 52 through 54' Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 153 through 162 Processing helix chain 'I' and resid 164 through 174 Processing helix chain 'J' and resid 4 through 21 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 50 through 72 removed outlier: 3.637A pdb=" N ALA J 72 " --> pdb=" O GLY J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 109 Processing helix chain 'J' and resid 137 through 145 removed outlier: 4.473A pdb=" N MET J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 170 removed outlier: 3.631A pdb=" N PHE J 164 " --> pdb=" O PHE J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 57 through 85 removed outlier: 4.392A pdb=" N ILE K 61 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR K 62 " --> pdb=" O PRO K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 3 through 22 removed outlier: 3.766A pdb=" N PHE L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.886A pdb=" N LEU L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 removed outlier: 3.768A pdb=" N SER L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP L 106 " --> pdb=" O GLN L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 154 removed outlier: 3.588A pdb=" N GLY L 148 " --> pdb=" O TRP L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 191 removed outlier: 4.214A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 204 removed outlier: 4.251A pdb=" N PHE L 203 " --> pdb=" O GLN L 199 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 224 removed outlier: 3.570A pdb=" N GLY L 215 " --> pdb=" O ILE L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 229 No H-bonds generated for 'chain 'L' and resid 227 through 229' Processing helix chain 'L' and resid 231 through 238 removed outlier: 3.597A pdb=" N SER L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 252 through 268 removed outlier: 4.150A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Proline residue: L 265 - end of helix removed outlier: 3.645A pdb=" N THR L 268 " --> pdb=" O PRO L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 292 Processing helix chain 'L' and resid 298 through 318 removed outlier: 3.531A pdb=" N ILE L 302 " --> pdb=" O ILE L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 322 through 349 removed outlier: 3.925A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 380 Processing helix chain 'L' and resid 388 through 400 removed outlier: 4.118A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 429 removed outlier: 3.614A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 Proline residue: L 453 - end of helix removed outlier: 5.336A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N PHE L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 3.593A pdb=" N THR L 508 " --> pdb=" O LEU L 504 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET L 509 " --> pdb=" O ASN L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 removed outlier: 3.513A pdb=" N PHE L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 4.785A pdb=" N HIS L 534 " --> pdb=" O SER L 531 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 605 Processing helix chain 'M' and resid 5 through 17 removed outlier: 4.006A pdb=" N LEU M 12 " --> pdb=" O SER M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 3.677A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 83 Proline residue: M 64 - end of helix removed outlier: 3.527A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix removed outlier: 4.517A pdb=" N ASN M 82 " --> pdb=" O MET M 78 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N HIS M 83 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 110 Processing helix chain 'M' and resid 115 through 136 removed outlier: 3.904A pdb=" N ILE M 120 " --> pdb=" O ILE M 116 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU M 123 " --> pdb=" O TYR M 119 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix removed outlier: 3.532A pdb=" N TRP M 136 " --> pdb=" O ILE M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 171 removed outlier: 3.627A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR M 152 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE M 158 " --> pdb=" O ILE M 155 " (cutoff:3.500A) Proline residue: M 159 - end of helix Processing helix chain 'M' and resid 176 through 182 Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.611A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 212 No H-bonds generated for 'chain 'M' and resid 210 through 212' Processing helix chain 'M' and resid 214 through 222 removed outlier: 3.985A pdb=" N LYS M 218 " --> pdb=" O LEU M 214 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 246 removed outlier: 6.329A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 257 Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.283A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 removed outlier: 3.844A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 367 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 414 removed outlier: 3.734A pdb=" N ILE M 411 " --> pdb=" O SER M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 449 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Proline residue: N 17 - end of helix Processing helix chain 'N' and resid 26 through 46 removed outlier: 3.721A pdb=" N ILE N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 121 removed outlier: 4.172A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 148 removed outlier: 4.198A pdb=" N ILE N 129 " --> pdb=" O HIS N 125 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN N 134 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix removed outlier: 3.587A pdb=" N ILE N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Proline residue: N 147 - end of helix Processing helix chain 'N' and resid 151 through 171 removed outlier: 3.768A pdb=" N LEU N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 194 Processing helix chain 'N' and resid 198 through 222 Proline residue: N 214 - end of helix removed outlier: 4.083A pdb=" N ASN N 222 " --> pdb=" O ALA N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 236 removed outlier: 3.794A pdb=" N LEU N 232 " --> pdb=" O ASN N 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP N 234 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 252 removed outlier: 3.940A pdb=" N THR N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 272 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 276 through 300 removed outlier: 4.119A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU N 288 " --> pdb=" O MET N 284 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN N 289 " --> pdb=" O MET N 285 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU N 290 " --> pdb=" O ALA N 286 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU N 296 " --> pdb=" O PHE N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 Processing helix chain 'N' and resid 324 through 334 Processing helix chain 'N' and resid 337 through 343 Proline residue: N 341 - end of helix Processing helix chain 'O' and resid 5 through 10 Processing helix chain 'O' and resid 14 through 16 No H-bonds generated for 'chain 'O' and resid 14 through 16' Processing helix chain 'O' and resid 35 through 46 Processing helix chain 'O' and resid 58 through 62 Processing helix chain 'O' and resid 71 through 74 No H-bonds generated for 'chain 'O' and resid 71 through 74' Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 92 through 118 Processing helix chain 'O' and resid 128 through 141 removed outlier: 4.380A pdb=" N PHE O 132 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL O 133 " --> pdb=" O TYR O 129 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N PHE O 134 " --> pdb=" O SER O 130 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 162 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 191 through 193 No H-bonds generated for 'chain 'O' and resid 191 through 193' Processing helix chain 'O' and resid 196 through 215 removed outlier: 4.481A pdb=" N LEU O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) Proline residue: O 212 - end of helix Processing helix chain 'O' and resid 225 through 228 No H-bonds generated for 'chain 'O' and resid 225 through 228' Processing helix chain 'O' and resid 231 through 239 Processing helix chain 'O' and resid 247 through 250 Processing helix chain 'O' and resid 253 through 264 Processing helix chain 'O' and resid 266 through 270 Processing helix chain 'O' and resid 272 through 274 No H-bonds generated for 'chain 'O' and resid 272 through 274' Processing helix chain 'O' and resid 286 through 298 removed outlier: 3.587A pdb=" N GLU O 298 " --> pdb=" O ASN O 294 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 308 No H-bonds generated for 'chain 'O' and resid 306 through 308' Processing helix chain 'P' and resid 29 through 41 removed outlier: 4.199A pdb=" N TYR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 61 removed outlier: 4.605A pdb=" N HIS P 58 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU P 61 " --> pdb=" O HIS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 84 Processing helix chain 'P' and resid 106 through 124 removed outlier: 4.353A pdb=" N ILE P 113 " --> pdb=" O VAL P 109 " (cutoff:3.500A) Proline residue: P 114 - end of helix Processing helix chain 'P' and resid 144 through 159 Processing helix chain 'P' and resid 179 through 186 removed outlier: 3.649A pdb=" N TYR P 185 " --> pdb=" O HIS P 181 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 197 Processing helix chain 'P' and resid 207 through 217 Processing helix chain 'P' and resid 221 through 223 No H-bonds generated for 'chain 'P' and resid 221 through 223' Processing helix chain 'P' and resid 238 through 248 Processing helix chain 'P' and resid 260 through 272 removed outlier: 3.602A pdb=" N LEU P 272 " --> pdb=" O LYS P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 288 Processing helix chain 'P' and resid 300 through 303 No H-bonds generated for 'chain 'P' and resid 300 through 303' Processing helix chain 'P' and resid 310 through 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 314 through 321 removed outlier: 5.422A pdb=" N ARG P 320 " --> pdb=" O GLU P 316 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N HIS P 321 " --> pdb=" O VAL P 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 45 Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.597A pdb=" N GLN S 30 " --> pdb=" O PRO S 27 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLY S 31 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL S 32 " --> pdb=" O SER S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 46 Processing helix chain 'S' and resid 83 through 94 removed outlier: 3.835A pdb=" N ALA S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU S 94 " --> pdb=" O MET S 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 21 Processing helix chain 'T' and resid 44 through 58 Processing helix chain 'T' and resid 64 through 69 removed outlier: 5.023A pdb=" N LYS T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 80 Processing helix chain 'U' and resid 8 through 21 Processing helix chain 'U' and resid 44 through 58 Processing helix chain 'U' and resid 64 through 69 removed outlier: 4.033A pdb=" N LYS U 69 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 84 Processing helix chain 'V' and resid 19 through 36 removed outlier: 3.594A pdb=" N LYS V 35 " --> pdb=" O LEU V 31 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS V 36 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 60 Processing helix chain 'V' and resid 64 through 71 Processing helix chain 'V' and resid 76 through 96 removed outlier: 3.941A pdb=" N LYS V 95 " --> pdb=" O ARG V 91 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 51 removed outlier: 3.913A pdb=" N ARG W 32 " --> pdb=" O ASN W 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG W 33 " --> pdb=" O GLU W 29 " (cutoff:3.500A) Proline residue: W 46 - end of helix Processing helix chain 'W' and resid 58 through 72 removed outlier: 3.927A pdb=" N ASN W 72 " --> pdb=" O MET W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 96 Processing helix chain 'W' and resid 102 through 108 removed outlier: 4.094A pdb=" N ARG W 107 " --> pdb=" O THR W 103 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE W 108 " --> pdb=" O HIS W 104 " (cutoff:3.500A) Processing helix chain 'W' and resid 120 through 123 No H-bonds generated for 'chain 'W' and resid 120 through 123' Processing helix chain 'X' and resid 21 through 26 Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 37 through 49 Processing helix chain 'X' and resid 52 through 54 No H-bonds generated for 'chain 'X' and resid 52 through 54' Processing helix chain 'X' and resid 56 through 75 Processing helix chain 'X' and resid 78 through 90 Processing helix chain 'X' and resid 96 through 98 No H-bonds generated for 'chain 'X' and resid 96 through 98' Processing helix chain 'X' and resid 101 through 113 Processing helix chain 'Y' and resid 4 through 11 removed outlier: 4.015A pdb=" N TYR Y 10 " --> pdb=" O PHE Y 6 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N HIS Y 11 " --> pdb=" O PHE Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 19 through 43 Processing helix chain 'Y' and resid 50 through 81 Processing helix chain 'Y' and resid 88 through 106 Processing helix chain 'Y' and resid 109 through 132 Processing helix chain 'Z' and resid 32 through 96 removed outlier: 3.556A pdb=" N GLY Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Proline residue: Z 72 - end of helix Processing helix chain 'Z' and resid 120 through 124 Processing helix chain 'Z' and resid 129 through 137 Processing helix chain 'a' and resid 2 through 30 Proline residue: a 7 - end of helix removed outlier: 4.062A pdb=" N ILE a 18 " --> pdb=" O CYS a 15 " (cutoff:3.500A) Proline residue: a 19 - end of helix Processing helix chain 'a' and resid 42 through 55 Processing helix chain 'b' and resid 5 through 14 removed outlier: 3.600A pdb=" N ALA b 13 " --> pdb=" O LYS b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 33 Proline residue: b 32 - end of helix Processing helix chain 'b' and resid 36 through 47 removed outlier: 3.899A pdb=" N LYS b 39 " --> pdb=" O PRO b 36 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER b 42 " --> pdb=" O LYS b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 81 No H-bonds generated for 'chain 'b' and resid 78 through 81' Processing helix chain 'c' and resid 14 through 45 Processing helix chain 'd' and resid 2 through 4 No H-bonds generated for 'chain 'd' and resid 2 through 4' Processing helix chain 'd' and resid 16 through 20 removed outlier: 3.633A pdb=" N SER d 20 " --> pdb=" O GLU d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 58 through 96 removed outlier: 3.654A pdb=" N PHE d 74 " --> pdb=" O PHE d 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 25 through 27 No H-bonds generated for 'chain 'e' and resid 25 through 27' Processing helix chain 'e' and resid 33 through 43 Processing helix chain 'e' and resid 48 through 54 removed outlier: 4.078A pdb=" N LYS e 53 " --> pdb=" O THR e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 66 Processing helix chain 'e' and resid 69 through 88 Processing helix chain 'e' and resid 95 through 98 No H-bonds generated for 'chain 'e' and resid 95 through 98' Processing helix chain 'f' and resid 5 through 32 removed outlier: 5.069A pdb=" N TRP f 10 " --> pdb=" O ARG f 7 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL f 15 " --> pdb=" O HIS f 12 " (cutoff:3.500A) Proline residue: f 16 - end of helix removed outlier: 3.544A pdb=" N LYS f 32 " --> pdb=" O ASP f 29 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 63 Processing helix chain 'g' and resid 67 through 77 Processing helix chain 'g' and resid 81 through 101 removed outlier: 5.711A pdb=" N GLU g 85 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP g 86 " --> pdb=" O MET g 83 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 45 removed outlier: 4.253A pdb=" N THR h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) Proline residue: h 35 - end of helix Processing helix chain 'h' and resid 63 through 66 removed outlier: 3.630A pdb=" N TYR h 66 " --> pdb=" O HIS h 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 63 through 66' Processing helix chain 'h' and resid 70 through 79 Processing helix chain 'h' and resid 83 through 117 removed outlier: 3.850A pdb=" N ALA h 101 " --> pdb=" O GLU h 97 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 24 Processing helix chain 'i' and resid 68 through 73 Processing helix chain 'i' and resid 76 through 88 Processing helix chain 'j' and resid 19 through 42 Processing helix chain 'j' and resid 44 through 48 Processing helix chain 'k' and resid 24 through 26 No H-bonds generated for 'chain 'k' and resid 24 through 26' Processing helix chain 'k' and resid 33 through 44 removed outlier: 3.776A pdb=" N VAL k 37 " --> pdb=" O PRO k 33 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG k 44 " --> pdb=" O LYS k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 51 through 58 removed outlier: 4.613A pdb=" N TRP k 56 " --> pdb=" O ARG k 52 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 62 No H-bonds generated for 'chain 'k' and resid 60 through 62' Processing helix chain 'k' and resid 68 through 72 Processing helix chain 'k' and resid 76 through 92 Processing helix chain 'l' and resid 16 through 26 Processing helix chain 'l' and resid 54 through 56 No H-bonds generated for 'chain 'l' and resid 54 through 56' Processing helix chain 'l' and resid 80 through 83 No H-bonds generated for 'chain 'l' and resid 80 through 83' Processing helix chain 'l' and resid 97 through 120 Processing helix chain 'l' and resid 133 through 137 Processing helix chain 'm' and resid 19 through 22 Processing helix chain 'm' and resid 26 through 51 removed outlier: 3.636A pdb=" N GLN m 49 " --> pdb=" O GLU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 62 through 72 Processing helix chain 'm' and resid 76 through 78 No H-bonds generated for 'chain 'm' and resid 76 through 78' Processing helix chain 'm' and resid 83 through 117 Proline residue: m 96 - end of helix Processing helix chain 'n' and resid 11 through 29 Processing helix chain 'n' and resid 33 through 50 removed outlier: 3.524A pdb=" N LEU n 42 " --> pdb=" O TYR n 38 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N HIS n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 Processing helix chain 'n' and resid 101 through 105 Processing helix chain 'n' and resid 108 through 113 removed outlier: 3.706A pdb=" N MET n 113 " --> pdb=" O SER n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 115 through 142 removed outlier: 4.576A pdb=" N ASP n 133 " --> pdb=" O MET n 129 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG n 134 " --> pdb=" O GLU n 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 8 Processing helix chain 'o' and resid 42 through 47 Processing helix chain 'o' and resid 59 through 72 Processing helix chain 'o' and resid 80 through 111 Processing helix chain 'p' and resid 28 through 56 removed outlier: 4.079A pdb=" N TRP p 42 " --> pdb=" O LEU p 38 " (cutoff:3.500A) Proline residue: p 43 - end of helix Processing helix chain 'p' and resid 73 through 75 No H-bonds generated for 'chain 'p' and resid 73 through 75' Processing helix chain 'p' and resid 81 through 123 removed outlier: 3.838A pdb=" N GLU p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN p 119 " --> pdb=" O ARG p 115 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR p 120 " --> pdb=" O GLU p 116 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLN p 121 " --> pdb=" O GLY p 117 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLN p 122 " --> pdb=" O GLU p 118 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 141 Processing helix chain 'p' and resid 151 through 170 Processing helix chain 'r' and resid 53 through 55 No H-bonds generated for 'chain 'r' and resid 53 through 55' Processing helix chain 'r' and resid 59 through 61 No H-bonds generated for 'chain 'r' and resid 59 through 61' Processing helix chain 's' and resid 44 through 53 removed outlier: 3.631A pdb=" N SER s 53 " --> pdb=" O ASN s 49 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.903A pdb=" N TYR B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL B 98 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE B 154 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 74 through 82 removed outlier: 6.675A pdb=" N ASN C 95 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 78 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL C 93 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA C 80 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU C 91 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 48 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LYS C 108 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 50 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N TYR C 110 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N ILE C 52 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 173 through 177 removed outlier: 3.657A pdb=" N ARG C 182 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.777A pdb=" N LEU D 64 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N SER D 69 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N VAL D 73 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 361 through 367 Processing sheet with id= F, first strand: chain 'E' and resid 98 through 103 Processing sheet with id= G, first strand: chain 'F' and resid 92 through 96 removed outlier: 3.670A pdb=" N THR F 221 " --> pdb=" O TYR F 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 133 through 138 removed outlier: 6.290A pdb=" N ASP F 174 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE F 136 " --> pdb=" O ASP F 174 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE F 176 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE F 138 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL F 178 " --> pdb=" O ILE F 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'F' and resid 266 through 271 removed outlier: 3.618A pdb=" N GLU F 270 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 254 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL F 334 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 296 through 298 Processing sheet with id= K, first strand: chain 'G' and resid 8 through 13 Processing sheet with id= L, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= M, first strand: chain 'G' and resid 226 through 228 Processing sheet with id= N, first strand: chain 'G' and resid 343 through 345 removed outlier: 8.150A pdb=" N CYS G 344 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA G 317 " --> pdb=" O CYS G 344 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET G 521 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE G 318 " --> pdb=" O MET G 521 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE G 523 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL G 559 " --> pdb=" O TYR G 545 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N GLY G 547 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU G 561 " --> pdb=" O GLY G 547 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 405 through 409 removed outlier: 3.614A pdb=" N VAL G 380 " --> pdb=" O VAL G 452 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY G 454 " --> pdb=" O VAL G 380 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN G 491 " --> pdb=" O VAL G 451 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 572 through 574 Processing sheet with id= Q, first strand: chain 'I' and resid 67 through 69 Processing sheet with id= R, first strand: chain 'I' and resid 94 through 100 removed outlier: 6.346A pdb=" N GLU I 99 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR I 108 " --> pdb=" O GLU I 99 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 61 through 64 Processing sheet with id= T, first strand: chain 'L' and resid 67 through 70 removed outlier: 6.862A pdb=" N LEU L 76 " --> pdb=" O TRP L 68 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'O' and resid 219 through 224 removed outlier: 3.714A pdb=" N ALA O 168 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL O 122 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL O 27 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU O 124 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLY O 29 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS O 49 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLU O 125 " --> pdb=" O LYS O 49 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N TYR O 51 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'P' and resid 128 through 131 removed outlier: 4.025A pdb=" N VAL P 90 " --> pdb=" O VAL P 20 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN P 44 " --> pdb=" O ALA P 21 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL P 23 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE P 46 " --> pdb=" O VAL P 23 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'P' and resid 165 through 168 Processing sheet with id= X, first strand: chain 'P' and resid 191 through 193 Processing sheet with id= Y, first strand: chain 'R' and resid 50 through 52 Processing sheet with id= Z, first strand: chain 'R' and resid 56 through 59 Processing sheet with id= AA, first strand: chain 'S' and resid 17 through 22 removed outlier: 7.985A pdb=" N VAL S 20 " --> pdb=" O PRO S 51 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU S 53 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU S 22 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG S 55 " --> pdb=" O LEU S 22 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'S' and resid 63 through 67 2799 hydrogen bonds defined for protein. 7656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.12 Time building geometry restraints manager: 22.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 26284 1.40 - 1.63: 38078 1.63 - 1.85: 840 1.85 - 2.07: 0 2.07 - 2.30: 80 Bond restraints: 65282 Sorted by residual: bond pdb=" C4 FMN F 502 " pdb=" C4A FMN F 502 " ideal model delta sigma weight residual 1.390 1.659 -0.269 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C5A FMN F 502 " pdb=" C9A FMN F 502 " ideal model delta sigma weight residual 1.390 1.579 -0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C5A FMN F 502 " pdb=" C6 FMN F 502 " ideal model delta sigma weight residual 1.390 1.575 -0.185 2.00e-02 2.50e+03 8.55e+01 bond pdb=" C2 FMN F 502 " pdb=" O2 FMN F 502 " ideal model delta sigma weight residual 1.230 1.399 -0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" C6 GTP O 401 " pdb=" O6 GTP O 401 " ideal model delta sigma weight residual 1.230 1.394 -0.164 2.00e-02 2.50e+03 6.70e+01 ... (remaining 65277 not shown) Histogram of bond angle deviations from ideal: 72.88 - 87.32: 76 87.32 - 101.76: 263 101.76 - 116.20: 43503 116.20 - 130.63: 44270 130.63 - 145.07: 342 Bond angle restraints: 88454 Sorted by residual: angle pdb=" C6 FMN F 502 " pdb=" C5A FMN F 502 " pdb=" N5 FMN F 502 " ideal model delta sigma weight residual 120.00 145.07 -25.07 3.00e+00 1.11e-01 6.98e+01 angle pdb=" C11 CDL g 201 " pdb=" CA5 CDL g 201 " pdb=" OA6 CDL g 201 " ideal model delta sigma weight residual 111.33 121.73 -10.40 1.32e+00 5.72e-01 6.19e+01 angle pdb=" C11 CDL d 201 " pdb=" CA5 CDL d 201 " pdb=" OA6 CDL d 201 " ideal model delta sigma weight residual 111.33 121.59 -10.26 1.32e+00 5.72e-01 6.02e+01 angle pdb=" C11 CDL L 702 " pdb=" CA5 CDL L 702 " pdb=" OA6 CDL L 702 " ideal model delta sigma weight residual 111.33 121.11 -9.78 1.32e+00 5.72e-01 5.48e+01 angle pdb=" PA NAP P 501 " pdb=" O3 NAP P 501 " pdb=" PN NAP P 501 " ideal model delta sigma weight residual 128.45 106.96 21.49 3.00e+00 1.11e-01 5.13e+01 ... (remaining 88449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 37988 35.70 - 71.40: 1440 71.40 - 107.10: 111 107.10 - 142.79: 15 142.79 - 178.49: 3 Dihedral angle restraints: 39557 sinusoidal: 16786 harmonic: 22771 Sorted by residual: dihedral pdb=" CB CYS p 76 " pdb=" SG CYS p 76 " pdb=" SG CYS p 83 " pdb=" CB CYS p 83 " ideal model delta sinusoidal sigma weight residual 93.00 164.27 -71.27 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CA ILE M 116 " pdb=" C ILE M 116 " pdb=" N MET M 117 " pdb=" CA MET M 117 " ideal model delta harmonic sigma weight residual 180.00 144.85 35.15 0 5.00e+00 4.00e-02 4.94e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual -102.41 76.09 -178.49 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 39554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.255: 9683 4.255 - 8.511: 0 8.511 - 12.766: 0 12.766 - 17.021: 0 17.021 - 21.277: 24 Chirality restraints: 9707 Sorted by residual: chirality pdb="FE2 SF4 B 201 " pdb=" S1 SF4 B 201 " pdb=" S3 SF4 B 201 " pdb=" S4 SF4 B 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.72 21.28 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 F 501 " pdb=" S1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S4 SF4 F 501 " both_signs ideal model delta sigma weight residual False -10.55 10.58 -21.14 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 G 802 " pdb=" S2 SF4 G 802 " pdb=" S3 SF4 G 802 " pdb=" S4 SF4 G 802 " both_signs ideal model delta sigma weight residual False -10.55 10.57 -21.13 2.00e-01 2.50e+01 1.12e+04 ... (remaining 9704 not shown) Planarity restraints: 11059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE h 34 " -0.044 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO h 35 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO h 35 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO h 35 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 74 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 75 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 108 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ASP P 108 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP P 108 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL P 109 " 0.013 2.00e-02 2.50e+03 ... (remaining 11056 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 299 2.45 - 3.06: 47382 3.06 - 3.68: 98611 3.68 - 4.29: 150715 4.29 - 4.90: 250099 Nonbonded interactions: 547106 Sorted by model distance: nonbonded pdb=" OG SER L 567 " pdb=" O2' LMT L 704 " model vdw 1.838 2.440 nonbonded pdb=" O LEU g 68 " pdb=" OG1 THR g 72 " model vdw 1.844 2.440 nonbonded pdb=" NZ LYS M 418 " pdb=" OE2 GLU n 91 " model vdw 1.955 2.520 nonbonded pdb=" OG SER m 15 " pdb=" OE1 GLU m 21 " model vdw 1.965 2.440 nonbonded pdb=" OG SER F 303 " pdb=" OH TYR F 354 " model vdw 1.975 2.440 ... (remaining 547101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'T' selection = (chain 'U' and (resid 7 through 82 or resid 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 20.450 Check model and map are aligned: 0.670 Set scattering table: 0.440 Process input model: 149.370 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.269 65282 Z= 0.508 Angle : 0.854 25.071 88454 Z= 0.418 Chirality : 1.048 21.277 9707 Planarity : 0.005 0.066 11059 Dihedral : 18.038 178.493 24839 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.07 % Favored : 93.80 % Rotamer: Outliers : 0.18 % Allowed : 18.36 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7698 helix: 1.23 (0.08), residues: 4231 sheet: -1.67 (0.25), residues: 376 loop : -0.87 (0.11), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 220 HIS 0.007 0.001 HIS P 37 PHE 0.029 0.002 PHE L 124 TYR 0.020 0.002 TYR B 122 ARG 0.008 0.001 ARG a 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15396 Ramachandran restraints generated. 7698 Oldfield, 0 Emsley, 7698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1145 time to evaluate : 5.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLU cc_start: 0.7942 (mp0) cc_final: 0.7735 (mp0) REVERT: B 135 TYR cc_start: 0.8987 (t80) cc_final: 0.7760 (t80) REVERT: C 177 ASP cc_start: 0.8570 (t0) cc_final: 0.8030 (t70) REVERT: D 356 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7683 (p90) REVERT: E 34 ILE cc_start: 0.8455 (mt) cc_final: 0.8232 (mm) REVERT: F 60 MET cc_start: 0.6247 (mmp) cc_final: 0.5810 (mmp) REVERT: F 106 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7923 (ptpp) REVERT: F 110 ILE cc_start: 0.8406 (mt) cc_final: 0.8133 (mt) REVERT: F 122 CYS cc_start: 0.8751 (m) cc_final: 0.8503 (m) REVERT: F 137 TYR cc_start: 0.7897 (t80) cc_final: 0.7622 (t80) REVERT: F 372 MET cc_start: 0.8016 (mtm) cc_final: 0.7796 (mtm) REVERT: G 521 MET cc_start: 0.5031 (ttp) cc_final: 0.4515 (mtp) REVERT: I 2 TYR cc_start: 0.8149 (p90) cc_final: 0.7395 (p90) REVERT: I 163 TRP cc_start: 0.8251 (m100) cc_final: 0.7778 (m100) REVERT: J 59 TYR cc_start: 0.8390 (m-80) cc_final: 0.7882 (m-80) REVERT: J 76 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7214 (pm20) REVERT: J 122 ASP cc_start: 0.7561 (m-30) cc_final: 0.7046 (m-30) REVERT: L 353 GLU cc_start: 0.7551 (tp30) cc_final: 0.7346 (tp30) REVERT: M 59 ASP cc_start: 0.6891 (m-30) cc_final: 0.6688 (m-30) REVERT: M 257 MET cc_start: 0.8586 (mmm) cc_final: 0.8180 (mmm) REVERT: M 271 MET cc_start: 0.8296 (mmp) cc_final: 0.7990 (mmp) REVERT: N 43 MET cc_start: 0.7907 (mmm) cc_final: 0.7669 (mmp) REVERT: N 243 MET cc_start: 0.8795 (mmm) cc_final: 0.8496 (mmm) REVERT: O 219 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7035 (mt-10) REVERT: P 269 LEU cc_start: 0.8135 (tt) cc_final: 0.7727 (mt) REVERT: P 306 GLN cc_start: 0.7527 (tm-30) cc_final: 0.6701 (tm-30) REVERT: R 92 LYS cc_start: 0.7572 (ttmm) cc_final: 0.6915 (ttmm) REVERT: S 30 GLN cc_start: 0.7057 (tp40) cc_final: 0.6788 (pm20) REVERT: S 65 TRP cc_start: 0.6053 (m100) cc_final: 0.5671 (m100) REVERT: S 80 ASN cc_start: 0.3906 (m110) cc_final: 0.3558 (m-40) REVERT: T 18 VAL cc_start: 0.8010 (t) cc_final: 0.7740 (t) REVERT: T 24 LYS cc_start: 0.7981 (mmmm) cc_final: 0.7682 (mmtt) REVERT: U 12 LYS cc_start: 0.8299 (tmtt) cc_final: 0.7994 (tmmt) REVERT: U 24 LYS cc_start: 0.8469 (mmmt) cc_final: 0.8038 (mmtm) REVERT: U 42 LEU cc_start: 0.7657 (mt) cc_final: 0.7441 (mm) REVERT: U 62 ILE cc_start: 0.8543 (mm) cc_final: 0.8251 (mm) REVERT: U 68 GLU cc_start: 0.7925 (pt0) cc_final: 0.7554 (mt-10) REVERT: V 56 ASP cc_start: 0.7400 (m-30) cc_final: 0.7147 (m-30) REVERT: Z 97 MET cc_start: 0.8269 (tpp) cc_final: 0.7798 (mmm) REVERT: b 15 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8023 (mm-30) REVERT: b 31 MET cc_start: 0.8853 (mmm) cc_final: 0.8527 (mmm) REVERT: c 24 SER cc_start: 0.9005 (m) cc_final: 0.8769 (m) REVERT: d 90 MET cc_start: 0.7775 (mmm) cc_final: 0.6926 (tpt) REVERT: g 25 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7400 (mm-40) REVERT: g 115 LYS cc_start: 0.8674 (mttm) cc_final: 0.8179 (mtpp) REVERT: h 140 THR cc_start: 0.8913 (m) cc_final: 0.8477 (p) REVERT: j 58 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7372 (tm-30) REVERT: k 20 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7045 (mp0) REVERT: k 26 GLN cc_start: 0.8846 (tt0) cc_final: 0.8645 (tt0) REVERT: k 73 LEU cc_start: 0.8460 (mt) cc_final: 0.8153 (mt) REVERT: l 41 MET cc_start: 0.7824 (mmm) cc_final: 0.7440 (tpp) REVERT: l 147 LYS cc_start: 0.7822 (mtmt) cc_final: 0.7535 (tmtt) REVERT: l 151 PRO cc_start: 0.7513 (Cg_endo) cc_final: 0.7231 (Cg_endo) REVERT: m 23 ASP cc_start: 0.8481 (t70) cc_final: 0.8130 (t0) REVERT: m 119 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7555 (mtpp) REVERT: r 51 ASN cc_start: 0.7509 (t0) cc_final: 0.6825 (t0) REVERT: s 40 TYR cc_start: 0.7712 (m-80) cc_final: 0.7442 (m-80) REVERT: s 44 THR cc_start: 0.7731 (m) cc_final: 0.7239 (m) outliers start: 12 outliers final: 5 residues processed: 1153 average time/residue: 0.6063 time to fit residues: 1203.9095 Evaluate side-chains 953 residues out of total 6839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 947 time to evaluate : 5.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain G residue 491 ASN Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 383 MET Chi-restraints excluded: chain P residue 109 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 761 random chunks: chunk 642 optimal weight: 0.6980 chunk 576 optimal weight: 0.0470 chunk 320 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 389 optimal weight: 0.8980 chunk 308 optimal weight: 0.7980 chunk 596 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 362 optimal weight: 10.0000 chunk 443 optimal weight: 5.9990 chunk 691 optimal weight: 10.0000 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: